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Ahmad K, Henikoff S, Ramachandran S. Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annu Rev Biochem 2022; 91:183-195. [PMID: 35303789 DOI: 10.1146/annurev-biochem-032620-104508] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene regulation arises out of dynamic competition between nucleosomes, transcription factors, and other chromatin proteins for the opportunity to bind genomic DNA. The timescales of nucleosome assembly and binding of factors to DNA determine the outcomes of this competition at any given locus. Here, we review how these properties of chromatin proteins and the interplay between the dynamics of different factors are critical for gene regulation. We discuss how molecular structures of large chromatin-associated complexes, kinetic measurements, and high resolution mapping of protein-DNA complexes in vivo set the boundary conditions for chromatin dynamics, leading to models of how the steady state behaviors of regulatory elements arise. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; .,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
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2
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Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods Mol Biol 2018; 1832:159-168. [PMID: 30073526 DOI: 10.1007/978-1-4939-8663-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The epigenome has been mapped in different cell types to understand the relationship between the chromatin landscape and the control of gene expression. Most mapping studies profile a large population of cells in various stages of the cell cycle, which results in an average snapshot of the chromatin landscape. However, chromatin is highly dynamic, undergoing rapid changes during active processes such as replication, transcription, repair, and remodeling. Hence, we need methods to map chromatin as a function of time. To address this problem in the context of replication, we developed the method MINCE-seq (Mapping In vivo Nascent Chromatin with EdU and sequencing). MINCE-seq is a genome-wide method that uses the passage of replication fork as a starting point to map the chromatin landscape as a function of time. MINCE-seq can measure chromatin dynamics in a time scale of minutes and at the resolution of individual nucleosome positions and transcription factor-binding sites genome-wide.
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Affiliation(s)
- Srinivas Ramachandran
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA.
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Petruk S, Cai J, Sussman R, Sun G, Kovermann SK, Mariani SA, Calabretta B, McMahon SB, Brock HW, Iacovitti L, Mazo A. Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation. Mol Cell 2017; 66:247-257.e5. [PMID: 28410996 DOI: 10.1016/j.molcel.2017.03.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/28/2016] [Accepted: 03/07/2017] [Indexed: 02/06/2023]
Abstract
Recruitment of transcription factors (TFs) to repressed genes in euchromatin is essential to activate new transcriptional programs during cell differentiation. However, recruitment of all TFs, including pioneer factors, is impeded by condensed H3K27me3-containing chromatin. Single-cell and gene-specific analyses revealed that, during the first hours of induction of differentiation of mammalian embryonic stem cells (ESCs), accumulation of the repressive histone mark H3K27me3 is delayed after DNA replication, indicative of a decondensed chromatin structure in all regions of the replicating genome. This delay provides a critical "window of opportunity" for recruitment of lineage-specific TFs to DNA. Increasing the levels of post-replicative H3K27me3 or preventing S phase entry inhibited recruitment of new TFs to DNA and significantly blocked cell differentiation. These findings suggest that recruitment of lineage-specifying TFs occurs soon after replication and is facilitated by a decondensed chromatin structure. This insight may explain the developmental plasticity of stem cells and facilitate their exploitation for therapeutic purposes.
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Affiliation(s)
- Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jingli Cai
- Department of Neuroscience, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Robyn Sussman
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Guizhi Sun
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sina K Kovermann
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Samanta A Mariani
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Steven B McMahon
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Lorraine Iacovitti
- Department of Neuroscience, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Annunziato AT. Assembling chromatin: the long and winding road. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:196-210. [PMID: 24459722 DOI: 10.1016/j.bbagrm.2011.07.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
It has been over 35 years since the acceptance of the "chromatin subunit" hypothesis, and the recognition that nucleosomes are the fundamental repeating units of chromatin fibers. Major subjects of inquiry in the intervening years have included the steps involved in chromatin assembly, and the chaperones that escort histones to DNA. The following commentary offers an historical perspective on inquiries into the processes by which nucleosomes are assembled on replicating and nonreplicating chromatin. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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Rodriguez J, Tsukiyama T. ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress. Genes Dev 2013; 27:74-86. [PMID: 23307868 DOI: 10.1101/gad.202978.112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Faithful DNA replication is essential for normal cell division and differentiation. In eukaryotic cells, DNA replication takes place on chromatin. This poses the critical question as to how DNA replication can progress through chromatin, which is inhibitory to all DNA-dependent processes. Here, we developed a novel genome-wide method to measure chromatin accessibility to micrococcal nuclease (MNase) that is normalized for nucleosome density, the NCAM (normalized chromatin accessibility to MNase) assay. This method enabled us to discover that chromatin accessibility increases specifically at and ahead of DNA replication forks in normal S phase and during replication stress. We further found that Mec1, a key regulatory ATR-like kinase in the S-phase checkpoint, is required for both normal chromatin accessibility around replication forks and replication fork rate during replication stress, revealing novel functions for the kinase in replication stress response. These results suggest a possibility that Mec1 may facilitate DNA replication fork progression during replication stress by increasing chromatin accessibility around replication forks.
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Affiliation(s)
- Jairo Rodriguez
- Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, Washington 98109, USA
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Benson LJ, Gu Y, Yakovleva T, Tong K, Barrows C, Strack CL, Cook RG, Mizzen CA, Annunziato AT. Modifications of H3 and H4 during chromatin replication, nucleosome assembly, and histone exchange. J Biol Chem 2006; 281:9287-96. [PMID: 16464854 DOI: 10.1074/jbc.m512956200] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Histone posttranslational modifications that accompany DNA replication, nucleosome assembly, and H2A/H2B exchange were examined in human tissue culture cells. Through microsequencing analysis and chromatin immunoprecipitation, it was found that a subset of newly synthesized H3.2/H3.3 is modified by acetylation and methylation at sites that correlate with transcriptional competence. Immunoprecipitation experiments suggest that cytosolic predeposition complexes purified from cells expressing FLAG-H4 contain H3/H4 dimers, not tetramers. Studies of the deposition of newly synthesized H2A/H2B onto replicating and nonreplicating chromatin demonstrated that H2A/H2B exchange takes place in chromatin regions that contain acetylated H4; however, there is no single pattern of H4 acetylation that accompanies exchange. H2A/H2B exchange is also largely independent of the deposition of replacement histone variant, H3.3. Finally, immunoprecipitation of nucleosomes replicated in the absence of de novo nucleosome assembly showed that histone modifications do not prevent the transfer of parental histones to newly replicated DNA and thus have the potential to serve as means of epigenetic inheritance. Our experiments provide an in-depth analysis of the "histone code" associated with chromatin replication and dynamic histone exchange in human cells.
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Affiliation(s)
- Laura J Benson
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA
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Annunziato AT. Split decision: what happens to nucleosomes during DNA replication? J Biol Chem 2005; 280:12065-8. [PMID: 15664979 DOI: 10.1074/jbc.r400039200] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Urnov FD. A feel for the template: zinc finger protein transcription factors and chromatin. Biochem Cell Biol 2003; 80:321-33. [PMID: 12123285 DOI: 10.1139/o02-084] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Transcription factors and chromatin collaborate in bringing the eukaryotic genome to life. An important, and poorly understood, aspect of this collaboration involves targeting the regulators to correct binding sites in vivo. An implicit and insufficiently tested assumption in the field has been that chromatin simply obstructs most sites and leaves only a few functionally relevant ones accessible. The major class of transcription factors in all metazoa, zinc finger proteins (ZFPs), can bind to chromatin in vitro (as clearly shown for Spl, GATA-1 and -4, and the nuclear hormone receptors, for example). Data on the accessibility of DNA within heterochromatin to nonhistone regulators (E.A. Sekinger and D.S. Gross. 2001. Mol. Cell 105: 403-414; C. Jolly et al. 2002. J. Cell. Biol. 156: 775-781) and the ability of the basal transcription machinery to reside within highly condensed chromatin (most recently, R. Christova and T. Oelgeschlaeger. 2002. Nat. Cell Biol. 4: 79-82) further weaken the argument that chromatin acts as an across-the-board deterrent to ZFP binding. These proteins, however, do not bind promiscuously in vivo, and recent data on human cells (C.E. Horak et al. 2002. Proc. Natl. Acad. Sci. U.S.A. 99: 2924-2929) confirm earlier data on budding yeast (B. Ren et al. 2000. Science (Washington, D.C.), 290: 2306-2309) that primary DNA sequence, i.e., density of binding sites per unit DNA length, is not the primary determinant of where a ZFP transcription factor will bind in vivo. This article reviews these data and uses ZFP transcription factors as a model system to compare in vitro binding to chromatin by transcription factors with their in vivo behavior in gene regulation. DNA binding domain structure, nonrandom nucleoprotein organization of chromatin at target promoters, and cooperativity of regulator action may all contribute to target site selection in vivo.
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Affiliation(s)
- Fyodor D Urnov
- Sangamo Biosciences, Pt Richmond Tech Centre, Richmond, CA 94804, USA.
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9
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Chafin DR, Vitolo JM, Henricksen LA, Bambara RA, Hayes JJ. Human DNA ligase I efficiently seals nicks in nucleosomes. EMBO J 2000; 19:5492-501. [PMID: 11032816 PMCID: PMC314012 DOI: 10.1093/emboj/19.20.5492] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The access to DNA within nucleosomes is greatly restricted for most enzymes and trans-acting factors that bind DNA. We report here that human DNA ligase I, which carries out the final step of Okazaki fragment processing and of many DNA repair pathways, can access DNA that is wrapped about the surface of a nucleosome in vitro and carry out its enzymatic function with high efficiency. In addition, we find that ligase activity is not affected by the binding of linker histone (H1) but is greatly influenced by the disposition of the core histone tail domains. These results suggest that the window of opportunity for human DNA ligase I may extend well beyond the first stages of chromatin reassembly after DNA replication or repair.
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Affiliation(s)
- D R Chafin
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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Perry CA, Allis CD, Annunziato AT. Parental nucleosomes segregated to newly replicated chromatin are underacetylated relative to those assembled de novo. Biochemistry 1993; 32:13615-23. [PMID: 8257695 DOI: 10.1021/bi00212a029] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibodies specific for acetylated histone H4 were used to examine the acetylation state of parental histones that segregate to newly replicated DNA. To generate newly replicated chromatin containing only segregated parental nucleosomes, isolated nuclei were labeled with [3H]TTP in vitro; alternatively, whole cells were labeled with [3H]thymidine in the presence of cycloheximide. Soluble chromatin was prepared by micrococcal nuclease digestion, and subjected to immunoprecipitation with "penta" antibodies (Lin et al., 1989). In sharp contrast to nucleosomes containing newly synthesized, diacetylated H4 (Perry et al., 1993), chromatin replicated in vitro was only marginally susceptible to immunoprecipitation. Control experiments established that bona fide acetylated chromatin was selectively immunoprecipitated by the same techniques and that segregated nucleosomes were not disassembled during treatment with "penta" antibodies. When replication was coupled to an in vitro histone acetylation system, the enrichment for segregated nucleosomes in the immunopellet increased approximately 3-fold, demonstrating that changes in the acetylation state of segregated histones can be detected immunologically and that parental histones on new DNA are accessible to acetyltransferases during, or immediately after, DNA replication. In vivo pulse-chase experiments, performed in the presence of cycloheximide, confirmed these results. Uptake experiments further established that concurrent histone acetylation did not alter the rate of DNA synthesis in vitro. Our results provide evidence that replication-competent chromatin is not obligatorily acetylated, and indicate that the acetylation status of segregated histones may be maintained during chromatin replication. The possible significance of this, with respect to the regulation of chromatin higher order structures during DNA replication, and the propagation of transcriptionally active vs inactive chromatin structures, is discussed.
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Affiliation(s)
- C A Perry
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02167
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11
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Sugasawa K, Murakami Y, Miyamoto N, Hanaoka F, Ui M. Assembly of nascent DNA into nucleosome structures in simian virus 40 chromosomes by HeLa cell extract. J Virol 1990; 64:4820-9. [PMID: 2168970 PMCID: PMC247970 DOI: 10.1128/jvi.64.10.4820-4829.1990] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A soluble system was developed that could support DNA replication in simian virus 40 (SV40) chromosomes. DNA synthesis in this system required the presence of purified SV40 large tumor antigen, SV40 chromosomes prepared from virus-infected monkey cells, a crude extract from HeLa cells, and several low-molecular-weight components. In comparison to the replication of purified SV40 form I DNA, the rate of DNA synthesis was 15 to 20% in this system. DNA synthesis started near the replication origin of SV40 and proceeded bidirectionally in a semiconservative manner. Micrococcal nuclease digestion experiments revealed that the replicated DNA produced in this system became organized into a regularly spaced array of nucleosome core particles when an appropriate amount of purified HeLa core histones was added to the reaction mixture. SV40 form I DNA replicating under the same conditions was also assembled into nucleosomes, which were arranged in a rather dispersed manner and formed an aberrant chromatin structure.
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Affiliation(s)
- K Sugasawa
- Department of Physiological Chemistry, Faculty of Pharmaceutical Sciences, University of Tokyo, Japan
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12
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Fotedar R, Roberts JM. Multistep pathway for replication-dependent nucleosome assembly. Proc Natl Acad Sci U S A 1989; 86:6459-63. [PMID: 2771936 PMCID: PMC297863 DOI: 10.1073/pnas.86.17.6459] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have used cell-free DNA replication to study the relationship between DNA replication and chromatin assembly. As others have reported, we find that DNA replication facilitates nucleosome assembly. We show here that replication-dependent nucleosome assembly occurs in at least two steps. The first step requires replicating DNA; the second step occurs after replication has been completed and is promoted by a nuclear extract. Consistent with this multistep model, we observe that the replicated simian virus 40 minichromosome is organized into a repeating array of DNA-protein particles that are structurally distinct from mature nucleosomes. These particles may be precursors in a pathway of nucleosome assembly since in the second, replication-independent step the nuclear extract converts this nascent chromatin into nucleosomes.
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Affiliation(s)
- R Fotedar
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98104
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13
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Subnuclear localization of proteins encoded by the oncogene v-myb and its cellular homolog c-myb. Mol Cell Biol 1987. [PMID: 3023837 DOI: 10.1128/mcb.6.1.62] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The retroviral transforming gene v-myb encodes a 45,000-Mr nuclear transforming protein (p45v-myb). p45v-myb is a truncated and mutated version of a 75,000-Mr protein encoded by the chicken c-myb gene (p75c-myb). Like its viral counterpart, p75c-myb is located in the cell nucleus. As a first step in identifying nuclear targets involved in cellular transformation by v-myb and in c-myb function, we determined the subnuclear locations of p45v-myb and p75c-myb. Approximately 80 to 90% of the total p45v-myb and p75c-myb present in nuclei was released from nuclei at low salt concentrations, exhibited DNA-binding activity, and was attached to nucleoprotein particles when released from the nuclei after digestion with nuclease. A minor portion of approximately 10 to 20% of the total p45v-myb and p75c-myb remained tightly associated with the nuclei even in the presence of 2 M NaCl. These observations suggest that both proteins are associated with two nuclear substructures tentatively identified as the chromatin and the nuclear matrix. The function of myb proteins may therefore depend on interactions with several nuclear targets.
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Klempnauer KH, Sippel AE. Subnuclear localization of proteins encoded by the oncogene v-myb and its cellular homolog c-myb. Mol Cell Biol 1986; 6:62-9. [PMID: 3023837 PMCID: PMC367484 DOI: 10.1128/mcb.6.1.62-69.1986] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The retroviral transforming gene v-myb encodes a 45,000-Mr nuclear transforming protein (p45v-myb). p45v-myb is a truncated and mutated version of a 75,000-Mr protein encoded by the chicken c-myb gene (p75c-myb). Like its viral counterpart, p75c-myb is located in the cell nucleus. As a first step in identifying nuclear targets involved in cellular transformation by v-myb and in c-myb function, we determined the subnuclear locations of p45v-myb and p75c-myb. Approximately 80 to 90% of the total p45v-myb and p75c-myb present in nuclei was released from nuclei at low salt concentrations, exhibited DNA-binding activity, and was attached to nucleoprotein particles when released from the nuclei after digestion with nuclease. A minor portion of approximately 10 to 20% of the total p45v-myb and p75c-myb remained tightly associated with the nuclei even in the presence of 2 M NaCl. These observations suggest that both proteins are associated with two nuclear substructures tentatively identified as the chromatin and the nuclear matrix. The function of myb proteins may therefore depend on interactions with several nuclear targets.
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15
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Annunziato AT, Seale RL. Presence of nucleosomes within irregularly cleaved fragments of newly replicated chromatin. Nucleic Acids Res 1984; 12:6179-96. [PMID: 6089109 PMCID: PMC320066 DOI: 10.1093/nar/12.15.6179] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In previous reports (Annunziato et al., J. Biol. Chem., 256:11880-11886 [1981]; Annunziato and Seale, Biochemistry 21:5431-5438 [1982]) we have described two classes of newly replicated chromatin which differ in structure, solubility properties, and requirements for maturation. One class is nucleosomal, soluble at low to intermediate ionic strengths, and acquires mature nucleosomal composition and normal repeat length in the absence of concurrent protein synthesis. In contrast, the other class is cleaved irregularly by MNase (appearing as a smear in DNA gels), is insoluble at moderate ionic strengths, requires protein synthesis to gain normal subunit structure, and comprises approximately 60% of total new chromatin DNA after mild nuclease digestion. It is now demonstrated that this heterogeneous component (produced by the action of either MNase or Hae III on chromatin replicated in cycloheximide) yields nucleosomes when redigested with MNase. The presence of nucleosomes within heterogeneous chromatin fragments suggests that nucleosomal and non-nucleosomal regions may be juxtaposed during chromatin replication. These findings are discussed with respect to current models of nucleosome segregation.
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Jakob KM, Ben Yosef S, Tal I. Reduced repeat length of nascent nucleosomal DNA is generated by replicating chromatin in vivo. Nucleic Acids Res 1984; 12:5015-24. [PMID: 6739296 PMCID: PMC318896 DOI: 10.1093/nar/12.12.5015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Micrococcal nuclease digestion of nuclei from sea urchin embryos revealed transient changes in chromatin structure which resulted in a reduction in the repeat length of nascent chromatin DNA as compared with bulk DNA. This was considered to be entirely the consequence of in vivo events at the replication fork (Cell 14, 259, 1978). However, a micrococcal nuclease-generated sliding of nucleosome cores relative to nascent DNA, which might account for the smaller DNA fragments, was not excluded. In vivo [3H]thymidine pulse-labeled nuclei were fixed with a formaldehyde prior to micrococcal nuclease digestion. This linked chromatin proteins to DNA and thus prevented any in vitro sliding of histone cores. All the nascent DNAs exhibiting shorter repeat lengths after micrococcal nuclease digestion, were resolved at identical mobilities in polyacrylamide gels of DNA from fixed and unfixed nuclei. We conclude that these differences in repeat lengths between nascent and bulk DNA was generated in vivo by changes in chromatin structure during replication, rather than by micrococcal nuclease-induced sliding of histone cores in vitro.
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Smith PA, Jackson V, Chalkley R. Two-stage maturation process for newly replicated chromatin. Biochemistry 1984; 23:1576-81. [PMID: 6722110 DOI: 10.1021/bi00302a036] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
HTC cells have been labeled by short exposures to [3H]thymidine in order to identify newly synthesized DNA. By either isolating nuclei directly or isolating them after an extensive fixation with formaldehyde, we have been able to identify two phases in the maturation process of newly replicated chromatin. The first phase which is relatively brief (less than 5 min) is reflected in a diffuse, irregular organization of nucleosomes on new DNA immediately postreplicatively . The second phase which lasts from 5 to 30 min postreplication is characterized by a normal repeat length for the nucleosomes which are nonetheless more weakly bound than bulk nucleosomes. This is reflected in increased sliding during nuclease digestion as well as increased nuclease sensitivity and the presence of easily dissociated histones which has been described by other workers.
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18
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Christman JK. DNA methylation in friend erythroleukemia cells: the effects of chemically induced differentiation and of treatment with inhibitors of DNA methylation. Curr Top Microbiol Immunol 1984; 108:49-78. [PMID: 6201322 DOI: 10.1007/978-3-642-69370-0_5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Annunziato AT, Seale RL. Histone deacetylation is required for the maturation of newly replicated chromatin. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44229-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Leffak IM. Chromatin assembled in the presence of cytosine arabinoside has a short nucleosome repeat. Nucleic Acids Res 1983; 11:5451-66. [PMID: 6889133 PMCID: PMC326290 DOI: 10.1093/nar/11.16.5451] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Incubation of MSB cells with cytosine arabinoside (1-beta-D-arabinofuranosylcytosine, ara-C) inhibits 3H-thymidine incorporation into nascent DNA while nucleosome core histone synthesis proceeds in molar stoichiometry at about 20% of control rates. The excess nascent histone is incorporated into chromatin and nucleosome cores are assembled normally on the small amount of DNA which is synthesized at submaximal levels of ara-C. This DNA becomes packaged into a shortened nucleosome repeat, however. These results indicate that the nucleosome core is a strongly conserved unit of chromatin replication and suggest that the stoichiometry of nascent histone to DNA may be one factor influencing the establishment of the nucleosome repeat length. It cannot be the only factor, however, since the closely packed nucleosomes made in the presence of ara-C begin to return to their normal spacing within six hours after reversal.
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21
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Künzler P, Stein A. Histone H5 can increase the internucleosome spacing in dinucleosomes to nativelike values. Biochemistry 1983; 22:1783-9. [PMID: 6849886 DOI: 10.1021/bi00277a007] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Chicken erythrocyte chromatin was assembled with inner histones at about 60% of the ratio found in vivo and subsequently incubated with histone H5 (or H1 + H5) in a solution containing 0.1 M NaCl and poly(glutamic acid). Micrococcal nuclease digestion produced dinucleosomes of 360-390 base pair (bp) DNA content, similar to those from native chromatin and contrasting with the 270-280 bp species found in material incubated without H5. On sucrose gradients a dinucleosome sedimenting at 16 S containing 360 bp DNA was isolated. Removal of H1 + H5 after reconstitution did not change these results; H5 thus can induce rearrangements of nucleosome cores with respect to their neighbors. The results are interpreted as an H5-induced "sliding apart" of histone octamers, complementary to the "sliding together" found in native chromatin after removal of H1 + H5.
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22
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Stein A, Künzler P. Histone H5 can correctly align randomly arranged nucleosomes in a defined in vitro system. Nature 1983; 302:548-50. [PMID: 6835386 DOI: 10.1038/302548a0] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In eukaryotic cells, DNA is packed into regularly spaced chromatin subunits called nucleosomes. The average distance between nucleosomes (the repeat length) varies in a tissue- and species-specific manner, with values ranging from about 160 to 240 DNA base pairs (bp). Thus, it has been recognized that the repeat length could be one of the factors underlying selective gene expression. In cells growing in culture, the characteristic repeat length for that type of cell seems to arise from an immature chromatin structure in which nucleosomes are initially irregularly spaced or are arranged in small closely packed clusters. At present no in vitro system has been described which is capable of reconstituting the mature physiological nucleosome spacing from purified chromatin components. Moreover, neither the factors necessary for spacing nor the reaction mechanism are known. We describe here an in vitro system that can restore the native subunit spacing in rearranged chromatin samples which have irregularly spaced nucleosomes similar to the situation apparent in newly replicated chromatin.
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Abstract
Many previously held concepts about the replication of chromatin have recently been revised, or seriously challenged. For instance, within the last two years, evidence has accumulated to indicate that newly synthesized DNA is not the sole site of deposition of newly synthesized histones, and that histones are not only made, but are assembled into chromatin in the absence of DNA synthesis. Furthermore, segregation of parental histones to daughter DNA duplexes may be bidirectional, rather than the previously accepted unidirectional mechanism. The storage of histones prior to assembly apparently involves histone pairs rather than octamers, and similarly, histones associate with DNA in (apparent) pairs, rather than as pre-assembled octameric units. It is currently questioned whether or not nucleoplasmin is involved in either histone storage or nucleosome assembly. The onset of histone synthesis has recently been found to occur in late G1 rather than in S, and thus is independent of DNA synthesis; however, the cessation of histone synthesis is linked to that of DNA. Thus, there emerges from this newly accumulated data the conclusion that chromatin biosynthesis is not as straightforward as was believed just a few years ago. As we review the evidence on each of these subjects, we attempt to point out directions for future experimentation.
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24
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Isolation of high mobility group-containing mononucleosomes from avian erythrocyte nuclei and their sensitivity to DNase I. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33626-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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25
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Sodium butyrate stimulates DNA repair in UV-irradiated normal and xeroderma pigmentosum human fibroblasts. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33468-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Association of newly synthesized histones with replicating and nonreplicating regions of chromatin. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34361-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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27
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Schlaeger EJ. Replicative conformation of parental nucleosomes: salt sensitivity of deoxyribonucleic acid-histone interaction and alteration of histone H1 binding. Biochemistry 1982; 21:3167-74. [PMID: 7104318 DOI: 10.1021/bi00256a021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The transiently altered DNA-histone interaction of parental chromatin during replication was studied by micrococcal nuclease digestion. A large amount of nuclease-resistant pulse-labeled DNA and a small fraction of nonreplicating DNA are released from chromatin fragments by treatment with 0.5 M NaCl and appear as protein-free DNA. As shown by reconstitution experiments, the salt sensitivity of digested nascent chromatin is most probably a consequence of the shorter DNA fragment size (55 +/- 15 base pairs) in these complexes. This new DNA is associated with parental chromatin fragments which are structurally changed in such a way that parts of nucleosomal DNA were more susceptible to nuclease attack. The core histones of these particles are probably not distinct from those of salt-stable nucleosomes. However, histone H1 and probably high-mobility group proteins appear to be more weakly bound during replication as shown by electrophoresis under nondenaturing conditions. The results agree with the assumption that the transient alteration of nucleosomal conformation describes a state in which DNA could be replicated without leaving the associated core histone complexes. A possible attachment of pulse-labeled chromatin with nuclear matrix is discussed.
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28
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Annunziato A, Schindler R, Thomas C, Seale R. Dual nature of newly replicated chromatin. Evidence for nucleosomal and non-nucleosomal DNA at the site of native replication forks. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68488-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Abstract
Following a labeling period of 2 min, HeLa histones continue to accumulate in chromatin for 10 min, indicating the presence of a histone pool. During the accumulation period, H2A and H2B enter chromatin immediately, while entry of H3 and H4 is more prolonged. Association of newly synthesized core histones with chromatin does not necessarily indicate assembly. When 2-min [3H]lysine-labeled chromatin is exposed to 0.45 M NaCl, nearly half of the newly synthesized histones are dissociated, while mature core histones are stable. H2A and 70% of H2B are salt stable and remain with newly synthesized polynucleosomes. About 30% of H2B, 50% of H4, and all of H3 are salt labile; thus, both the new nucleosomal core histones and salt-labile new core histones are nonstoichiometric. Pulse-labeled core histones are more trypsin-sensitive than mature histones. When the salt-labile, newly synthesized histones are removed, the remaining proteins have the same trypsin sensitivity as bulk core protein. Examination of the tryptic peptides indicated that the increased trypsin sensitivity was due to complete destruction of the loosely associated core histones which undergo a lag prior to assembly. The altered order of appearance of two peptides in stripped, newly assembled nucleosomes indicates that the conformation in these particles is different from that in mature chromatin.
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30
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Jackson V, Marshall S, Chalkley R. The sites of deposition of newly synthesized histone. Nucleic Acids Res 1981; 9:4563-81. [PMID: 7301583 PMCID: PMC327459 DOI: 10.1093/nar/9.18.4563] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The chromosomal fragments produced by nuclease digestion of freshly replicated chromatin migrate more rapidly relative to bulk chromatin when analyzed in nucleoprotein gels. The cause of the anomalous migration has been studied and the evidence indicates that rather than reflecting a shorter nucleosomal repeat in vivo that it may be a consequence of nucleosome sliding during the digestion itself. The distinct electrophoretic characteristics of nucleosomal material containing newly replicated DNA have enabled us to examine their histone composition by two dimensional electrophoresis. We find that nucleosomes containing new DNA also contain newly synthesized histones H3 and H4. In contrast more than 50% of newly synthesized H2A and H2B, and essentially all of new H1, are deposited at sites on the bulk chromatin distinct from that material containing newly replicated DNA. In addition we show that newly synthesized histones H3 and H4 are bound unusually weakly when they first become associated with the chromatin.
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31
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Galili G, Levy A, Jakob KM. Changes in chromatin structure at the replication fork. II The DNPs containing nascent DNA and a transient chromatin modification detected by DNAase I. Nucleic Acids Res 1981; 9:3991-4005. [PMID: 6272192 PMCID: PMC327410 DOI: 10.1093/nar/9.16.3991] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Discrete deoxyribonucleoproteins (DNPs) containing nascent and/or bulk DNA, were obtained by fractionating micrococcal nuclease digests of nuclei form 3H-thymidine pulse (15-20 sec) and 14C-thymidine long (16 h) labeled sea urchin embryos in polyacrylamide gels. One of these DNPs was shown to contain the micrococcal nuclease resistant 300 bp "large nascent DNA" described in Cell 14, 259-267, 1978. The bulk and nascent mononucleosome fractions provided evidence for the preferential digestion by micrococcal nuclease of nascent over bulk linker regions to yield mononucleosome cores with nascent DNA. DNAase I was used to probe whether any nascent DNA is in nucleosomes. Nascent as well as bulk single-stranded DNA fragments occurred in multiples of 10.4 bases with higher than random frequencies of certain fragment sizes (for instance 83 bases) as expected from a nucleosome structure. However, a striking background of nascent DNA between nascent DNA peaks was observed. This was eliminated by a pulse-chase treatment or by digestion of pulse-labeled nuclei with micrococcal nuclease together with DNAase I. One of several possible interpretations of these results suggests that a transient change in nucleosome structure may have created additional sites for the nicking of nascent DNA by DNAase I; the micrococcal nuclease sensitivity of the interpeak radioactivity suggest its origin from the linker region. Endogenous nuclease of sea urchin embryos cleaves chromatin DNA in a manner similar to that of DNAase I.
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32
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The large high mobility group proteins of rainbow trout are localized predominantly in the nucleus and nucleoli of a cultured trout cell line. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68916-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Harrington RE. Structural conformations of nucleosomes at low ionic strength from flow birefringence and intrinsic viscosity. Biopolymers 1981; 20:719-52. [PMID: 7225524 DOI: 10.1002/bip.1981.360200408] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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34
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Hohmann P. Histone gene expression: hybrid cells and organisms establish complex controls. INTERNATIONAL REVIEW OF CYTOLOGY 1981; 71:41-93. [PMID: 6786996 DOI: 10.1016/s0074-7696(08)61182-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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35
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36
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Abstract
Ehrlich ascites tumor (EAT) nucleosomes treated with increasing NaCl concentrations were analyzed by sucrose density gradient centrifugation. Two events were found to take place in the course of the salt treatment: a) increasing amounts of nucleosomes dissociated into free DNA and protein in the interval 0.6M-1.5M NaCl, and b) the sedimentation coefficient of the nucleosomes decreased from 11S to 8S in the interval 0.6M - 1M NaCl. This decrease was not caused by loss of protein and was fully reversible upon slow and gradual lowering of the ionic strength. This shows that before dissociation of the protein core from DNA, nucleosomes undergo a structural transition. The electron microscopic observations revealed that it consisted in detachment of the ends of nucleosomal DNA from the protein core. It is suggested that an arginine-rich domain in the protein core exists, which holds more tightly the central part of the nucleosomal DNA, while its ends are relatively loosely bound to lysine-rish domains.
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37
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Mukherjee AS, Duttagupta AK, Chatterjee SN, Chatterjee RN, Majumdar D, Chatterjee C, Ghosh M, Achary PM, Dey A, Banerjee I. Regulation of DNA replication in Drosophila. BASIC LIFE SCIENCES 1980; 16:57-83. [PMID: 6779808 DOI: 10.1007/978-1-4684-7968-3_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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38
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Palter K, Alberts B. The use of DNA-cellulose for analyzing histone-DNA interactions. Discovery of nucleosome-like histone binding to single-stranded DNA. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86644-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Seyedin S, Kistler W. Levels of chromosomal protein high mobility group 2 parallel the proliferative activity of testis, skeletal muscle, and other organs. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86480-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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40
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41
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Crémisi C. Chromatin replication revealed by studies of animal cells and papovaviruses (simian virus 40 and polyoma virus). Microbiol Rev 1979; 43:297-319. [PMID: 232241 PMCID: PMC281479 DOI: 10.1128/mr.43.3.297-319.1979] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Wist E, Prydz H. No stimulatory effect of added histones on DNA synthesis in isolated HeLa cell nuclei. Mol Biol Rep 1979; 5:189-91. [PMID: 492163 DOI: 10.1007/bf00778422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Contrary to some recent reports DNA synthesis in isolated HeLa cell nuclei was not stimulated by the addition of low amounts of histones neither in the presence nor in the absence of cytosol. The individual histone fractions H1, H2A, H2B and H3 also failed to stimulated DNA synthesis.
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43
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Schlaeger EJ, Knippers R. DNA-histone interaction in the vicinity of replication points. Nucleic Acids Res 1979; 6:645-56. [PMID: 424308 PMCID: PMC327718 DOI: 10.1093/nar/6.2.645] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chromatin replication was studied in isolated nuclei from Concanavalin A activated lymphocytes. Digestion with micrococcal nuclease revealed that the resistant fraction of in vitro replicated DNA is associated with nucleosomes. Earlier experiments had shown that the nuclease resistant fraction of nascent DNA is composed of fragments which are shorter than the nuclease resistant fragments of bulk DNA. In this communication we demonstrate that the short fragments of nascent DNA are differently bound to nucleosome like structures compared to bulk DNA. At 0.5 M NaCl a fraction of pulse labeled labeled DNA is released from these structures and appears as free double stranded DNA of about 140 base pair length (5S DNA) while the 185 pair fragments of mature replicated DNA remain attached to nucleosomes under these conditions. The experiments may indicate that the interaction of a fraction of replicating DNA with histones differs from that of bulk DNA.
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45
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Murphy RF, Wallace RB, Bonner J. Altered nucleosome spacing in newly replicated chromatin from Friend leukemia cells. Proc Natl Acad Sci U S A 1978; 75:5903-7. [PMID: 282612 PMCID: PMC393084 DOI: 10.1073/pnas.75.12.5903] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Chromatin from Friend leukemia cells labeled with [14C]thymidine for 24 hr followed by [3H]thymidine for 10 min is converted into nucleosomes by staphylococcal nuclease at only half the rate that total chromatin is converted. Polyacrylamide gel electrophoresis of nucleosomal DNA from cells labeled for 24 hr with [14C]thymidine followed by 10 min with [3H]thymidine demonstrates that the internucleosomal spacer of newly replicated chromatin is approximately 20 base pairs shorter than that of total chromatin. The implications of this difference for models of chromatin structure are discussed.
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